Fits the Yule Model to a Phylogenetic Tree

Usage

Arguments

phy

an object of class "phylo".

use.root.edge

a logical specifying whether to consider the root
edge in the calculations.

Details

The tree must be fully dichotomous.

The maximum likelihood estimate of the speciation rate is obtained by
the ratio of the number of speciation events on the cumulative number
of species through time; these two quantities are obtained with the
number of nodes in the tree, and the sum of the branch lengths,
respectively.

If there is a `root.edge' element in the phylogenetic tree, and
use.root.edge = TRUE, then it is assumed that it has a
biological meaning and is counted as a branch length, and the root is
counted as a speciation event; otherwise the number of speciation
events is the number of nodes - 1.

The standard-error of lambda is computed with the second derivative of
the log-likelihood function.

Value

An object of class "yule" which is a list with the following
components: